Phylogenetic diversity and comparative historical demography within a species complex of Indo-West Pacific Saccostrea oysters

Taxonomic uncertainties, often arising from cryptic species or lineages, present a significant impediment to wildlife conservation. This problem has been partially alleviated by the advent of DNA barcoding. Uncovering unrecognized sympatric species/lineages, in turn, provides an opportunity to examine their respective responses to potentially shared historical environmental oscillations within a comparative phylogeographic and demographic framework. Based on four mitochondrial genes, we detailed the phylogenetic diversity of a species complex within the genus Saccostrea Dollfus and Dautzenberg, 1920—a group of tropical and subtropical oysters—along the coasts of Ishigaki and Iriomote Islands in the Ryukyu Island Arc, Japan. We further assessed mitochondrial diversity and historical demography for each identified lineage to evaluate the impacts of the Last Glacial Maximum (LGM) on their population trajectories. Our survey revealed nine distinct lineages, including one previously unrecorded. This finding, combined with known lineages, brings the total to at least 12 lineages within the Ryukyu Island Arc. These lineages were generally characterized by elevated mitochondrial diversity and non-star-like haplotype networks, indicative of long-term population stability. Our demographic reconstructions based on Bayesian skyline plot analyses further suggested that population sizes remained stable throughout the LGM. By integrating these findings with regional paleoceanographic context, we discuss the mechanisms underlying this apparent population stability.